Genetic analysis of selected strains of eastern oyster (Crassostrea virginica Gmelin) using AFLP and microsatellite

Abstract: Amplified fragment length polymorphisms (AFLPs) and microsatellite markers were used to examine genetic variation and divergence in 4 selected strains (DBH, NEH, FMF, and CTS) and 1 wild population (DBW) of the eastern oyster Crassostrea virginica Gmelin. Eighty-six AFLP markers (from 3 primer pairs) and 5 microsatellite loci were used for the analysis of 30 oysters from each of the 5 populations. Microsatellite loci were considerably more variable than AFLPs. The observed heterozygosity ranged from 0.560 to 0.640 across populations for microsatellites, and from 0.186 to 0.207 for AFLPs. Both F st and / PT of microsatellite data and / PT statistics of AFLP data revealed significant divergence between all pairs of populations. There was no significant reduction in heterozygosity in all 4 selected strains; however, the number of alleles per locus was considerably lower in the selected strains than in the wild population. Two strains subjected to long-term selection for disease resistance shared frequency shifts at a few loci, which deserve further analysis to determine if they are linked to disease-resistance genes

The Potential for Oysters, Crassostrea Virginica, to Develop Resistance to Dermo Disease in the Field: Evaluation Using a Gene-Based Population Dynamics Model

Today, populations of eastern oysters, Crassostrea virginica, are commonly limited by disease mortality. Resistance to MSX disease has developed in a number of cases, but the development of resistance to Dermo disease would appear to be limited, despite the high mortality rates and frequency of epizootics. Can aspects of the host\u27s genetics or population dynamics limit the response to the disease despite the apparent opportunity afforded by alleles conferring disease resistance or tolerance? To answer this question, we use a gene-based population dynamics model, configured for C. virginica, to simulate the development of disease resistance using mortality as the agent of selection. Simulated populations were exposed to 4 levels of mortality covering the range in mortality observed in Delaware Bay in the l990s. In each case, disease resistance increased in the simulated population over time, normally proportional to the increase in mortality rate imposed by the disease. However, simulations show that the population responds even at its most rapid rate on multidecadal to half-century timescales. As the mortality rate declines with increasing disease resistance, the rate of further improvement in disease resistance likewise declines. Thus, disease resistance develops over decadal timescales at a 40%-per-year mortality rate, but, as mortality rate falls to 25% per year, the rate of further development of disease resistance extends to half-century timescales. The discouraging profundity is that a mortality rate of 25% per year, yielding a rate of selection profoundly slow, is still very high. In northern climes, significant decrements in oyster abundance will occur. Evidence from fisheries retrospectives suggests that oysters cannot withstand a constant removal at this scale without compromising population integrity noticeably. So, a mortality rate that grievously limits the development of disease resistance still sorely strains the species\u27 ability to maintain a vibrant population necessary to its long-term survival

Effective population sizes of eastern oyster Crassostrea virginica (Gmelin) populations in Delaware Bay, USA

Effective population size (Ne) is an important concept in population genetics as it dictates the rate of genetic change caused by drift. Ne estimates for many marine populations are small relative to the census population size. Small Ne in a large population may indicate high reproductive variance or sweepstakes reproductive success (SRS). The eastern oyster (Crassostrea virginica) may be prone to SRS due to its high fecundity and high larval mortality. To examine if SRS occurs in the eastern oyster, we studied Ne and genetic variation of oyster populations in Delaware Bay. Adult and spat oysters were collected from five locations in different years and genotyped with seven microsatellite markers. Slight genetic differences were revealed by Fst statistics between the adult populations and spat recruits, while the adult populations are spatially homogeneous and temporally stable. Comparisons of genetic diversity and relatedness among adult and spat samples failed to provide convincing evidence for strong SRS. Ne estimates obtained with five different methods were variable, small and often without upper confidence limits. For single sample collections, Ne estimates for spat (140–440) were consistently smaller than that for adults (589–2,779). Analysis of pooled adult samples across all sites suggests that Ne for the whole bay may be very large, as indicated by the large point estimates and the lack of upper confidence limits. These results suggest that Ne may be small for a given spat fall, but the entire adult population may have large Ne and is temporally stable as it is the accumulation of many spat falls per year over many year

Multiple drivers of interannual oyster settlement and recruitment in the lower Chesapeake Bay

Despite global investment in shellfish restoration activities, relatively little attention has been given to predicting optimal restoration sites and testing these expectations. We used a coupled biological-physical connectivity model as a guide to plant two distinct hatchery-spawned strains of the eastern oyster, Crassostrea virginica, in the Lafayette River, Virginia during the summer of 2013 at two locations corresponding to virtual spawning locations within the connectivity model. We utilized single nucleotide polymorphism markers to test the model predictions by genotyping oysters recruited after planting two hatchery-spawned strains and examining interannual recruitment variability for two successive years. Two spat were identified as hybrids of one of the planted strains and resident oyster genotypes. We also observed a genetic influence from an oyster strain used previously for restoration. Differences in environmental conditions between the two years of monitored recruitment likely affected larval dispersal and survival, contributing to observed interannual differences in the newly recruiting cohorts. Oyster spat from 2013 were genetically more similar to resident adults sampled in the Lafayette River, while the 2014 spat exhibited genotypic frequencies more similar to adults from surrounding rivers. The winds during the spawning seasons differed between years providing conditions for retention in 2013 and mixing of water masses in 2014. We recommend that the monitoring of restoration activities should consider relevant environmental conditions and observe multiple years of recruitment to assess the genetic impacts of restoration plantings and variable reproductive success

Can Oysters Crassostrea virginica Develop Resistance to Dermo Disease in the Field: The Impediment Posed by Climate Cycles

Populations of eastern oysters, Crassostrea virginica, are commonly limited by mortality from dermo disease. Little development of resistance to Perkinsus marinus, the dermo pathogen, has occurred, despite the high mortality rates and frequency of epizootics. Can the tendency of the parasite to exhibit cyclic epizootics limit the oyster\u27s response to the disease despite the presence of alleles apparently conferring disease resistance? We utilize a gene-based population dynamics model to simulate the development of disease resistance in Crassostrea virginica populations exposed to cyclic mortality encompassing periodicities expected of dermo disease over the geographic range at which epizootics have been observed. Cyclic disease reduces the incremental rate of development of disease resistance profoundly, primarily as a consequence of a reduction in the time-integrated population mortality rate, which will be about half the cycle\u27s apogean rate. Cyclicity enhances host survival for more susceptible genotypes at cycle nadir. Moreover, alleles conferring disease resistance typically are rare in the naive population. Cyclicity permits these rare alleles to drift and most often, that drift is towards lower frequencies because fewer animals carrying these alleles predestines a lower probability of their successful dissemination during sweepstakes reproduction at cycle nadir. Variations in population dynamics, such as differences in abundance, fecundity at size, and in the number of individuals successfully producing recruits varied the outcome little. The large number of loci contributing to disease resistance, the cyclic nature of the exposure relieving the population in predictable time units from selection pressure, and the tendency for conditions that might enhance development of disease resistance such as rapid growth to be counterbalanced by multiple yearly spawnings, hamper the rapid development of disease resistance. Unfortunately, epizootic mortality rates at cycle apogee, twice that observed at cycle nadir or prior to onset of disease, are consequential from the standpoint of population sustainability, but much less consequential for driving selection towards disease resistance. The periodicity of dermo epizootics may doom oyster populations to an extended period of low abundance, during which disease resistance slowly improves; bit by bit limiting the depredations of the disease

The Shortest Duration Constrained Hidden Markov Model: data denoise and forecast optimization on the country-product matrix for the Fitness-Complexity Algorithm

The Economic Fitness Index describes industrial completeness and comprehensively reflects product diversification with competitiveness and product complexity in production globalization. The Fitness-Complexity Algorithm offers a scientific approach to predicting GDP and obtains fruitful results. As a recursion algorithm, the non-linear iteration processes give novel insights into product complexity and country fitness without noise data. However, the Country-Product Matrix and Revealed Comparative Advantage data have abnormal noises which contradict the relative stability of product diversity and the transformation of global production. The data noise entering the iteration algorithm, combined with positively related Fitness and Complexity, will be amplified in each recursion step. We introduce the Shortest Duration Constrained Hidden Markov Model (SDC-HMM) to denoise the Country-Product Matrix for the first time. After the country-product matrix test, the country case test, the noise estimation test and the panel regression test of national economic fitness indicators to predict GDP growth, we show that the SDC-HMM could reduce abnormal noise by about 25% and identify change points. This article provides intra-sample predictions that theoretically confirm that the SDC-HMM can improve the effectiveness of economic fitness indicators in interpreting economic growth

Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia

<p>Abstract</p> <p>Background</p> <p>Oysters are morphologically plastic and hence difficult subjects for taxonomic and evolutionary studies. It is long been suspected, based on the extraordinary species diversity observed, that Asia Pacific is the epicenter of oyster speciation. To understand the species diversity and its evolutionary history, we collected five <it>Crassostrea </it>species from Asia and sequenced their complete mitochondrial (mt) genomes in addition to two newly released Asian oysters (<it>C. iredalei </it>and <it>Saccostrea mordax</it>) for a comprehensive analysis.</p> <p>Results</p> <p>The six Asian <it>Crassostrea </it>mt genomes ranged from 18,226 to 22,446 bp in size, and all coded for 39 genes (12 proteins, 2 rRNAs and 25 tRNAs) on the same strand. Their genomes contained a split of the <it>rrnL </it>gene and duplication of <it>trnM</it>, <it>trnK </it>and <it>trnQ </it>genes. They shared the same gene order that differed from an Atlantic sister species by as many as nine tRNA changes (6 transpositions and 3 duplications) and even differed significantly from <it>S. mordax </it>in protein-coding genes. Phylogenetic analysis indicates that the six Asian <it>Crassostrea </it>species emerged between 3 and 43 Myr ago, while the Atlantic species evolved 83 Myr ago.</p> <p>Conclusions</p> <p>The complete conservation of gene order in the six Asian <it>Crassostrea </it>species over 43 Myr is highly unusual given the remarkable rate of rearrangements in their sister species and other bivalves. It provides strong evidence for the recent speciation of the six <it>Crassostrea </it>species in Asia. It further indicates that changes in mt gene order may not be strictly a function of time but subject to other constraints that are presently not well understood.</p

Constraining the interacting dark energy models from weak gravity conjecture and recent observations

We examine the effectiveness of the weak gravity conjecture in constraining the dark energy by comparing with observations. For general dark energy models with plausible phenomenological interactions between dark sectors, we find that although the weak gravity conjecture can constrain the dark energy, the constraint is looser than that from the observations.Comment: 14 pages, 12 figures, revtex4, v2: minor corrections, accepted for publication in PL

The Effect of Self-Assembling Peptide RADA16-I on the Growth of Human Leukemia Cells in Vitro and in Nude Mice

Nanofiber scaffolds formed by self-assembling peptide RADA16-I have been used for the study of cell proliferation to mimic an extracellular matrix. In this study, we investigated the effect of RADA16-I on the growth of human leukemia cells in vitro and in nude mice. Self-assembly assessment showed that RADA16-I molecules have excellent self-assembling ability to form stable nanofibers. MTT assay displayed that RADA16-I has no cytotoxicity for leukemia cells and human umbilical vein endothelial cells (HUVECs) in vitro. However, RADA16-I inhibited the growth of K562 tumors in nude mice. Furthermore, we found RADA16-I inhibited vascular tube-formation by HUVECs in vitro. Our data suggested that nanofiber scaffolds formed by RADA16-I could change tumor microenvironments, and inhibit the growth of tumors. The study helps to encourage further design of self-assembling systems for cancer therapy.China. Ministry of Education (project 985